Animals, including humans, host a multitude of microbes (collectively referred to as the host's microbiota) in anatomical locations including the mouth, esophagus, stomach, small intestine, large intestine, caecum, colon, rectum, vagina, skin, nasal cavities, ear, and lungs. The human microbiota is responsible for a multitude of critical processes, including development of the immune system, metabolism of carbohydrates, proteins, and xenobiotics formation and regeneration of the epithelium, fat storage, production of hormones, production of vitamins, and protection from pathogen infections, among others (Hooper L V, Gordon J I. Science. 2001;292:1115; Rakoff-Nahoum S, Paglino J, Eslami-Varzaneh F, Edberg S, Medzhitov R. Cell. 2004;118:229; Backhed F, et al. Proc. Natl. Acad. Sci. U.S.A. 2004;101:15718; Stappenbeck T S, Hooper L V, Gordon J I. Proc. Natl. Acad. Sci. U.S.A. 2002;99:15451;1 Sonnenburg J L, Angenent L T, Gordon J I. Nat. Immunol. 2004;5:569; Hooper L V, et al. Science. 2001; 291:881). Alterations of the human microbiota, which can be caused by a number of factors such as antibiotic use, excessive hygiene, diet, genetic background, or combinations of the above, have been associated with a number of infectious diseases (e.g., C. difficile infections), inflammatory, autoimmune, and allergic diseases (e.g., ulcerative colitis, Crohn's disease, Type ldiabetes, food allergies, asthma, rheumatoid arthritis), and metabolic diseases (e.g., Type 2 diabetes, metabolic syndrome, obesity, malnutrition), among others. These alterations can lead to a loss of tolerance against benign food antigens or benign commensal bacterial antigens, subsequent excessive inflammatory responses, metabolic dysregulation, and damage to the intestinal tissue, which compromises its ability to serve as a barrier between the gut lumen and the systemic circulation. Approaches for countering the harmful effects of microbiota alterations on health are limited, despite the key role that such alterations play in promoting human pathology. Interventions known to modulate the microbiota include antibiotics, prebiotics, probiotics and fecal transplants, each of which has limited effects and potential adverse effects. Additional approaches to countering the detrimental effects of microbiome alterations on human health which are efficacious are clearly needed, particularly compositions that can be manufactured with the quality standards of a pharmaceutical product.